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1.

SOD1 Phosphorylation by mTORC1 Couples Nutrient Sensing and Redox Regulation.

Tsang, Chi Kwan; Chen, Miao; Cheng, Xin; Qi, Yanmei; Chen, Yin; Das, Ishani; Li, Xiaoxing; Vallat, Brinda; Fu, Li-Wu; Qian, Chao-Nan; Wang, Hui-Yun; White, Eileen; Burley, Stephen K; Zheng, X F Steven.

Mol Cell ; 70(3): 502-515.e8, 2018 05 03.

Article in English | MEDLINE | ID: mdl-29727620

2.

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.

Burley, Stephen K; Bhikadiya, Charmi; Bi, Chunxiao; Bittrich, Sebastian; Chao, Henry; Chen, Li; Craig, Paul A; Crichlow, Gregg V; Dalenberg, Kenneth; Duarte, Jose M; Dutta, Shuchismita; Fayazi, Maryam; Feng, Zukang; Flatt, Justin W; Ganesan, Sai; Ghosh, Sutapa; Goodsell, David S; Green, Rachel Kramer; Guranovic, Vladimir; Henry, Jeremy; Hudson, Brian P; Khokhriakov, Igor; Lawson, Catherine L; Liang, Yuhe; Lowe, Robert; Peisach, Ezra; Persikova, Irina; Piehl, Dennis W; Rose, Yana; Sali, Andrej; Segura, Joan; Sekharan, Monica; Shao, Chenghua; Vallat, Brinda; Voigt, Maria; Webb, Ben; Westbrook, John D; Whetstone, Shamara; Young, Jasmine Y; Zalevsky, Arthur; Zardecki, Christine.

Nucleic Acids Res ; 51(D1): D488-D508, 2023 01 06.

Article in English | MEDLINE | ID: mdl-36420884

3.

Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain.

Staquicini, Daniela I; Tang, Fenny H F; Markosian, Christopher; Yao, Virginia J; Staquicini, Fernanda I; Dodero-Rojas, Esteban; Contessoto, Vinícius G; Davis, Deodate; O'Brien, Paul; Habib, Nazia; Smith, Tracey L; Bruiners, Natalie; Sidman, Richard L; Gennaro, Maria L; Lattime, Edmund C; Libutti, Steven K; Whitford, Paul C; Burley, Stephen K; Onuchic, José N; Arap, Wadih; Pasqualini, Renata.

Proc Natl Acad Sci U S A ; 118(30)2021 07 27.

Article in English | MEDLINE | ID: mdl-34234013

4.

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection.

Markosian, Christopher; Staquicini, Daniela I; Dogra, Prashant; Dodero-Rojas, Esteban; Lubin, Joseph H; Tang, Fenny H F; Smith, Tracey L; Contessoto, Vinícius G; Libutti, Steven K; Wang, Zhihui; Cristini, Vittorio; Khare, Sagar D; Whitford, Paul C; Burley, Stephen K; Onuchic, José N; Pasqualini, Renata; Arap, Wadih.

Mol Biol Evol ; 39(5)2022 05 03.

Article in English | MEDLINE | ID: mdl-35511693

5.

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies.

Segura, Joan; Rose, Yana; Bittrich, Sebastian; Burley, Stephen K; Duarte, Jose M.

Bioinformatics ; 38(12): 3304-3305, 2022 06 13.

Article in English | MEDLINE | ID: mdl-35543462

6.

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB.

Bittrich, Sebastian; Rose, Yana; Segura, Joan; Lowe, Robert; Westbrook, John D; Duarte, Jose M; Burley, Stephen K.

Bioinformatics ; 38(5): 1452-1454, 2022 02 07.

Article in English | MEDLINE | ID: mdl-34864908

7.

Integrative illustration for coronavirus outreach.

Goodsell, David S; Voigt, Maria; Zardecki, Christine; Burley, Stephen K.

PLoS Biol ; 18(8): e3000815, 2020 08.

Article in English | MEDLINE | ID: mdl-32760062

8.

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.

Sehnal, David; Bittrich, Sebastian; Deshpande, Mandar; Svobodová, Radka; Berka, Karel; Bazgier, Václav; Velankar, Sameer; Burley, Stephen K; Koca, Jaroslav; Rose, Alexander S.

Nucleic Acids Res ; 49(W1): W431-W437, 2021 07 02.

Article in English | MEDLINE | ID: mdl-33956157

9.

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.

Burley, Stephen K; Bhikadiya, Charmi; Bi, Chunxiao; Bittrich, Sebastian; Chen, Li; Crichlow, Gregg V; Christie, Cole H; Dalenberg, Kenneth; Di Costanzo, Luigi; Duarte, Jose M; Dutta, Shuchismita; Feng, Zukang; Ganesan, Sai; Goodsell, David S; Ghosh, Sutapa; Green, Rachel Kramer; Guranovic, Vladimir; Guzenko, Dmytro; Hudson, Brian P; Lawson, Catherine L; Liang, Yuhe; Lowe, Robert; Namkoong, Harry; Peisach, Ezra; Persikova, Irina; Randle, Chris; Rose, Alexander; Rose, Yana; Sali, Andrej; Segura, Joan; Sekharan, Monica; Shao, Chenghua; Tao, Yi-Ping; Voigt, Maria; Westbrook, John D; Young, Jasmine Y; Zardecki, Christine; Zhuravleva, Marina.

Nucleic Acids Res ; 49(D1): D437-D451, 2021 01 08.

Article in English | MEDLINE | ID: mdl-33211854

10.

Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development.

Burley, Stephen K.

J Biol Chem ; 296: 100559, 2021.

Article in English | MEDLINE | ID: mdl-33744282

11.

RCSB Protein Data Bank 1D tools and services.

Segura, Joan; Rose, Yana; Westbrook, John; Burley, Stephen K; Duarte, Jose M.

Bioinformatics ; 36(22-23): 5526-5527, 2021 Apr 01.

Article in English | MEDLINE | ID: mdl-33313665

12.

Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.

Shao, Chenghua; Feng, Zukang; Westbrook, John D; Peisach, Ezra; Berrisford, John; Ikegawa, Yasuyo; Kurisu, Genji; Velankar, Sameer; Burley, Stephen K; Young, Jasmine Y.

Glycobiology ; 31(9): 1204-1218, 2021 09 20.

Article in English | MEDLINE | ID: mdl-33978738

13.

Real-time structural motif searching in proteins using an inverted index strategy.

Bittrich, Sebastian; Burley, Stephen K; Rose, Alexander S.

PLoS Comput Biol ; 16(12): e1008502, 2020 12.

Article in English | MEDLINE | ID: mdl-33284792

14.

Real time structural search of the Protein Data Bank.

Guzenko, Dmytro; Burley, Stephen K; Duarte, Jose M.

PLoS Comput Biol ; 16(7): e1007970, 2020 07.

Article in English | MEDLINE | ID: mdl-32639954

15.

BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.

Sehnal, David; Bittrich, Sebastian; Velankar, Sameer; Koca, Jaroslav; Svobodová, Radka; Burley, Stephen K; Rose, Alexander S.

PLoS Comput Biol ; 16(10): e1008247, 2020 10.

Article in English | MEDLINE | ID: mdl-33075050

16.

How to help the free market fight coronavirus.

Burley, Stephen K.

Nature ; 580(7802): 167, 2020 04.

Article in English | MEDLINE | ID: mdl-32210376

17.

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.

Burley, Stephen K; Berman, Helen M; Bhikadiya, Charmi; Bi, Chunxiao; Chen, Li; Di Costanzo, Luigi; Christie, Cole; Dalenberg, Ken; Duarte, Jose M; Dutta, Shuchismita; Feng, Zukang; Ghosh, Sutapa; Goodsell, David S; Green, Rachel K; Guranovic, Vladimir; Guzenko, Dmytro; Hudson, Brian P; Kalro, Tara; Liang, Yuhe; Lowe, Robert; Namkoong, Harry; Peisach, Ezra; Periskova, Irina; Prlic, Andreas; Randle, Chris; Rose, Alexander; Rose, Peter; Sala, Raul; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John; Woo, Jesse; Yang, Huanwang; Young, Jasmine; Zhuravleva, Marina; Zardecki, Christine.

Nucleic Acids Res ; 47(D1): D464-D474, 2019 01 08.

Article in English | MEDLINE | ID: mdl-30357411

18.

BioJava 5: A community driven open-source bioinformatics library.

Lafita, Aleix; Bliven, Spencer; Prlic, Andreas; Guzenko, Dmytro; Rose, Peter W; Bradley, Anthony; Pavan, Paolo; Myers-Turnbull, Douglas; Valasatava, Yana; Heuer, Michael; Larson, Matt; Burley, Stephen K; Duarte, Jose M.

PLoS Comput Biol ; 15(2): e1006791, 2019 02.

Article in English | MEDLINE | ID: mdl-30735498

19.

D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Parks, Conor D; Gaieb, Zied; Chiu, Michael; Yang, Huanwang; Shao, Chenghua; Walters, W Patrick; Jansen, Johanna M; McGaughey, Georgia; Lewis, Richard A; Bembenek, Scott D; Ameriks, Michael K; Mirzadegan, Tara; Burley, Stephen K; Amaro, Rommie E; Gilson, Michael K.

J Comput Aided Mol Des ; 34(2): 99-119, 2020 02.

Article in English | MEDLINE | ID: mdl-31974851

20.

Predicting Proteome-Scale Protein Structure with Artificial Intelligence.

Burley, Stephen K; Arap, Wadih; Pasqualini, Renata.

N Engl J Med ; 385(23): 2191-2194, 2021 12 02.

Article in English | MEDLINE | ID: mdl-34874637

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